Fix compare functions

Compare functions were set up to use an old version of clade.freq, and
were barfing.  It's fixed now.
Create parse.clades

Created parse.clades.R, containing the parse.clades function.  This
function takes a vector of clades given as tip numbers (e.g., the
cladetable attribute of many of our analyses) and a multiphylo object
and returns a vector of clades with those numbers converted to names.
Names are taken from the multiphylo object.